Contacts of the strand formed by residues 194 - 203 (chain Q) in PDB entry 4R2G
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 194 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162Q ASP 3.1 3.8 + - - -
163Q TYR* 2.8 62.9 + - + +
164Q PHE* 4.0 24.4 - + - -
165Q PRO* 4.2 1.8 - - + -
166Q GLU* 3.4 52.9 - - + -
186Q ALA* 4.2 5.2 - - + -
187Q VAL 3.2 7.0 - - - +
188Q LEU* 3.3 52.7 - - + +
193Q LEU* 1.3 69.9 - - - +
195Q SER* 1.3 64.4 + - - +
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Residues in contact with SER 195 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178P TYR* 3.7 9.6 + - - -
159Q LEU* 6.0 0.2 - - - -
160Q VAL 3.1 12.1 - - - -
161Q LYS* 3.5 25.9 - - - +
162Q ASP 3.0 10.7 + - - -
163Q TYR* 3.8 0.2 - - - -
187Q VAL* 3.1 39.8 + - - +
189Q GLN* 3.0 30.0 + - - -
194Q TYR* 1.3 72.0 - - - +
196Q LEU* 1.3 59.7 + - - +
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Residues in contact with LEU 196 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178P TYR* 3.6 3.6 - - - -
159Q LEU* 3.9 1.9 - - - +
160Q VAL* 2.9 45.9 + - + +
163Q TYR* 3.0 26.6 - - + +
166Q GLU* 5.5 1.3 - - + +
168Q VAL* 4.0 24.2 - - + +
170Q VAL* 4.1 10.3 - - + -
183Q THR* 3.5 21.5 - - + -
184Q PHE 3.6 17.5 - - - +
185Q PRO 4.6 1.1 - - - -
186Q ALA* 3.7 15.5 - - + +
195Q SER* 1.3 74.6 - - - +
197Q SER* 1.3 95.2 + - - +
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Residues in contact with SER 197 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134P VAL* 3.7 14.0 - - - +
136P LEU* 4.7 12.3 - - - -
178P TYR* 2.6 26.6 + - - -
142Q LEU* 4.8 3.6 - - - -
158Q CYS 3.4 12.3 - - - -
159Q LEU* 3.4 18.8 - - - +
160Q VAL* 4.8 0.4 - - - +
184Q PHE* 2.9 33.9 + - - +
196Q LEU* 1.3 84.7 + - - +
198Q SER* 1.3 61.8 + - - +
199Q VAL* 5.9 0.2 - - - -
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Residues in contact with SER 198 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157Q GLY* 3.1 22.2 - - - -
158Q CYS* 3.1 15.7 + - - -
170Q VAL* 3.5 28.7 - - - +
172Q TRP* 3.3 24.1 + - - -
181Q VAL* 3.8 2.9 - - - +
182Q HIS 4.2 0.2 - - - -
183Q THR* 3.2 26.3 + - - +
184Q PHE* 4.9 0.2 - - - -
197Q SER* 1.3 78.4 - - - +
199Q VAL* 1.3 61.5 + - - +
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Residues in contact with VAL 199 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117P THR* 5.3 4.5 - - + +
119P PHE* 3.9 24.0 - - + -
136P LEU* 3.5 24.2 - - + -
142Q LEU* 5.2 3.6 - - + -
155Q ALA* 5.1 7.9 - - + -
156Q LEU 3.4 12.3 - - - +
157Q GLY* 4.5 2.5 - - - -
172Q TRP* 4.6 0.7 - - - -
181Q VAL* 3.6 3.3 - - - +
182Q HIS* 2.8 37.6 + - + +
184Q PHE* 3.8 24.0 - - + -
197Q SER 4.4 0.2 - - - -
198Q SER* 1.3 77.4 - - - +
200Q VAL* 1.3 68.0 + - - +
201Q THR* 6.4 1.3 - - + -
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Residues in contact with VAL 200 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154Q ALA 3.9 1.0 - - - +
155Q ALA* 3.6 4.0 - - - -
156Q LEU* 3.1 42.7 + - + +
172Q TRP* 3.7 29.6 - - + +
177Q LEU* 4.1 25.4 - - + -
179Q SER 5.4 0.9 - - - -
180Q GLY 3.3 21.1 - - - +
181Q VAL* 4.2 7.0 - - + +
199Q VAL* 1.3 79.7 - - - +
201Q THR* 1.3 76.8 + - - +
202Q VAL* 3.8 8.3 + - + +
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Residues in contact with THR 201 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153Q THR* 4.8 15.0 - - - +
154Q ALA 4.1 4.9 - - - +
155Q ALA* 4.1 17.5 - - + +
179Q SER 5.1 0.9 - - - +
180Q GLY* 3.5 21.4 + - - +
199Q VAL* 5.8 1.5 - - + +
200Q VAL* 1.3 78.6 - - - +
202Q VAL* 1.3 65.9 + - - +
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Residues in contact with VAL 202 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153Q THR* 4.0 7.4 - - - -
154Q ALA 2.8 36.5 + - - +
156Q LEU* 3.6 31.0 - - + -
177Q LEU* 5.0 5.6 - - + -
200Q VAL* 4.0 10.8 - - + +
201Q THR* 1.3 78.6 - - - +
203Q PRO* 1.4 82.0 - - + +
206Q SER* 4.9 0.2 - - - -
207Q LEU* 5.2 1.7 - - + +
212Q TYR* 2.8 39.7 - - + +
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Residues in contact with PRO 203 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152Q GLY 3.3 8.5 - - - +
153Q THR* 4.1 8.3 - - + -
202Q VAL* 1.4 101.9 - - + +
204Q SER* 1.3 60.1 + - - +
205Q SER* 3.9 12.6 - - - +
206Q SER* 3.2 37.3 + - - +
207Q LEU* 3.8 9.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il